MolNFT v1 · #189732 · protein
Cytidine bound structure of pseudouridine kinase (puki) from escherichia COLI strain B
7VTF: “Cytidine bound structure of pseudouridine kinase (puki) from escherichia COLI strain B”. X-ray diffraction, 1 ligand (CTN), 9 pockets (best druggability 0.70). MolNFT v1 #189732 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7VTF
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine kinase
- EC
- 2.7.1.83
- UniProt
- A0A1V3W5E1
- Ligands
- CTN
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudouridine kinase (EC 2.7.1.83) | protein | 301 | 38% helix, 24% strand | A0A1V3W5E1 |
| B, C | Pseudouridine kinase (EC 2.7.1.83) | protein | 302 | 37% helix, 24% strand | A0A1V3W5E1 |
| D | Pseudouridine kinase (EC 2.7.1.83) | protein | 299 | 39% helix, 24% strand | A0A1V3W5E1 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.70 | 0.76 | 74 | CTN |
| 2 | 712 | 0.69 | 0.77 | 62 | CTN |
| 3 | 655 | 0.68 | 0.77 | 59 | CTN |
| 4 | 650 | 0.68 | 0.76 | 58 | CTN |
| 5 | 76 | 0.53 | 0.85 | 22 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1732 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1672 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VTF · cytidine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1V3W5E1
- Elsewhere: RCSB PDB 7VTF · PDBe 7VTF · UniProt A0A1V3W5E1
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